Mitochondrial genome architecture in non-alcoholic fatty liver disease.

Non-alcoholic fatty liver disease (NAFLD) is associated with mitochondrial dysfunction, a decreased liver mitochondrial DNA (mtDNA) content, and impaired energy metabolism. To understand the clinical implications of mtDNA diversity in the biology of NAFLD, we applied deep-coverage whole sequencing of the liver mitochondrial genomes. We used a multistage study design, including a discovery phase, a phenotype-oriented study to assess the mutational burden in patients with steatohepatitis at different stages of liver fibrosis, and a replication study to validate findings in loci of interest. We also assessed the potential protein-level impact of the observed mutations. To determine whether the observed changes are tissue-specific, we compared the liver and the corresponding peripheral blood entire mitochondrial genomes. The nuclear genes POLG and POLG2 (mitochondrial DNA polymerase-γ) were also sequenced. We observed that the liver mtDNA of patients with NAFLD harbours complex genomes with a significantly higher mutational (1.28-fold) rate and degree of heteroplasmy than in controls. The analysis of liver mitochondrial genomes of patients with different degrees of fibrosis revealed that the disease severity is associated with an overall 1.4-fold increase in mutation rate, including mutations in genes of the oxidative phosphorylation (OXPHOS) chain. Significant differences in gene and protein expression patterns were observed in association with the cumulative number of OXPHOS polymorphic sites. We observed a high degree of homology (∼98%) between the blood and liver mitochondrial genomes. A missense POLG p.Gln1236His variant was associated with liver mtDNA copy number. In conclusion, we have demonstrated that OXPHOS genes contain the highest number of hotspot positions associated with a more severe phenotype. The variability of the mitochondrial genomes probably originates from a common germline source; hence, it may explain a fraction of the 'missing heritability' of NAFLD. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Telomere length in the two extremes of abnormal fetal growth and the programming effect of maternal arterial hypertension.

We tested the hypothesis that leukocyte telomere length (LTL) is associated with birth weight in both extremes of abnormal fetal growth: small (SGA) and large for gestational age newborns (LGA). Clinical and laboratory variables of the mothers and the neonates were explored; 45 newborns with appropriate weight for gestational age (AGA), 12 SGA and 12 LGA were included. Whether the differences might be explained by variation in OBFC1 (rs9419958) and CTC1 (rs3027234) genes associated with LTL was determined. A significant association between birth weight and LTL was observed; LTL was significantly shorter in LGA newborns (1.01 ± 0.12) compared with SGA (1.73 ± 0.19) p < 0.005, mean ± SE. Maternal (Spearman R = -0.6, p = 0.03) and neonatal LTL (R = -0.25, p = 0.03) were significantly and inversely correlated with maternal history of arterial hypertension in previous gestations. Neonatal LTL was not significantly associated with either rs9419950 or rs3027234, suggesting that the association between neonatal LTL and birth weight is not influenced by genetic variation in genes that modify the interindividual LTL. In conclusion, telomere biology seems to be modulated by abnormal fetal growth; modifications in telomere length might be programmed by an adverse environment in utero.

Fetal metabolic programming and epigenetic modifications: a systems biology approach.

A growing body of evidence supports the notion that epigenetic changes such as DNA methylation and histone modifications, both involving chromatin remodeling, contribute to fetal metabolic programming. We use a combination of gene-protein enrichment analysis resources along with functional annotations and protein interaction networks for an integrative approach to understanding the mechanisms underlying fetal metabolic programming. Systems biology approaches suggested that fetal adaptation to an impaired nutritional environment presumes profound changes in gene expression that involve regulation of tissue-specific patterns of methylated cytosine residues, modulation of the histone acetylation-deacetylation switch, cell differentiation, and stem cell pluripotency. The hypothalamus and the liver seem to be differently involved. In addition, new putative explanations have emerged about the question of whether in utero overnutrition modulates fetal metabolic programming in the same fashion as that of a maternal environment of undernutrition, suggesting that the mechanisms behind these two fetal nutritional imbalances are different. In conclusion, intrauterine growth restriction is most likely to be associated with the induction of persistent changes in tissue structure and functionality. Conversely, a maternal obesogenic environment is most probably associated with metabolic reprogramming of glucose and lipid metabolism, as well as future risk of metabolic syndrome (MS), fatty liver, and insulin (INS) resistance.

Epigenetic modification of liver mitochondrial DNA is associated with histological severity of nonalcoholic fatty liver disease.

OBJECTIVE & DESIGN: Nonalcoholic fatty liver disease (NAFLD) is a clinical condition that refers to progressive histological changes ranging from simple steatosis (SS) to nonalcoholic steatohepatitis (NASH). We evaluated the status of cytosine methylation (5mC) of liver mitochondrial DNA (mtDNA) in selected regions of the mtDNA genome, such as D-loop control region, and mitochondrially encoded NADH dehydrogenase 6 (MT-ND6) and cytochrome C oxidase I (MT-CO1), to contrast the hypothesis that epigenetic modifications play a role in the phenotypic switching from SS to NASH. METHODS: We studied liver biopsies obtained from patients with NAFLD in a case-control design; 45 patients and 18 near-normal liver-histology subjects. RESULTS: MT-ND6 methylation was higher in the liver of NASH than SS patients (p < 0.04) and MT-ND6 methylated DNA/unmethylated DNA ratio was significantly associated with NAFLD activity score (p < 0.02). Liver MT-ND6 mRNA expression was significantly decreased in NASH patients (0.26 ± 0.30) versus SS (0.74 ± 0.48), p < 0.003, and the protein level was also diminished. The status of liver MT-ND6 methylation in NASH group was inversely correlated with the level of regular physical activity (R = -0.54, p < 0.02). Hepatic methylation levels of D-Loop and MT-CO1 were not associated with the disease severity. DNA (cytosine-5) methyltransferase 1 was significantly upregulated in NASH patients (p < 0.002). Ultrastructural evaluation showed that NASH is associated with mitochondrial defects and peroxisome proliferation. CONCLUSION: Hepatic methylation and transcriptional activity of the MT-ND6 are associated with the histological severity of NAFLD. Epigenetic changes of mtDNA are potentially reversible by interventional programs, as physical activity could modulate the methylation status of MT-ND6.

Liver transcriptional profile of atherosclerosis-related genes in human nonalcoholic fatty liver disease.

OBJECTIVES AND DESIGN: Epidemiological studies have suggested a role of nonalcoholic fatty liver disease (NAFLD) in the development of cardiovascular disease. We evaluated liver mRNA expression of 84 genes encoding proteins involved in the atherosclerosis pathway in patients with NAFLD proven through biopsy in a case-control design, and examined the putative role of the histological disease severity in the molecular events associated with the atherogenic profile. RESULTS: Nonalcoholic steatohepatitis (NASH), when compared with simple steatosis (SS), significantly increases the expression of TGFB1 (6.8, p<0.005), angiotensin I-converting enzyme (ACE) (2.1, p<0.007), LAMA1 (2.1, p<0.007), SERPINB2 (2.1, p<0.007), CSF2 (2.5, p<0.002), IL1A (2.5, p<0.005), IL3 (2.1, p<0.007), IL4 (2.1, p<0.007), LIF (2.1, p<0.007), and MMP1 (2.1, p<0.007), and decreases the transcript levels of genes involved in the negative regulation of cell-death pathways. A post hoc analysis of liver biopsies of NASH patients who were treated with enalapril monotherapy because of arterial hypertension showed a significant association with lower fibrosis scores in comparison with untreated patients. BIRC3, a severe hypoxia-activated gene, was significantly increased in SS (8.2, p<0.004), when compared with the controls. NASH, but not SS, was also associated with a significant increase in platelet abundance of TGFB1 mRNA. Systems biology analysis revealed highly scored pathways involved in the regulation of programmed cell death, angiogenesis, and immune system, in which TGFB1 was mostly involved. CONCLUSION: NASH, but not SS, may increase atherosclerotic and cardiovascular risk by local overexpression of mediators of atherogenesis, endothelial damage, and regulators of blood pressure; this observation may have therapeutic implications, because ACE inhibitors may improve both cardiovascular outcomes and liver fibrosis. Hepatocyte hypoxia seems to have an important role in the molecular events activated by liver steatosis.

Mitochondrial DNA copy number is modulated by genetic variation in the signal transducer and activator of transcription 3 (STAT3).

The regulation of mitochondrial DNA (mtDNA) copy number not only is critical for the maintenance of the normal mitochondrial function but has a strong clinical significance. A recent report revealed that the signal transducer and activator of transcription 3 (STAT3) is involved in the regulation of the mitochondrial function and is required for the optimal function of the electron transport chain. In this study, we explored whether gene variants in the STAT3 influence the leukocyte mtDNA copy number. Clinical data and blood samples were collected from 179 subjects (aged 52.8 ± 0.9 years). Mitochondrial DNA quantification using nuclear DNA (nDNA) as a reference was carried out by a real-time quantitative polymerase chain reaction method; results are presented as the mtDNA/nDNA ratio. We selected 3 tag single nucleotide polymorphisms showing a minor allele frequency greater than 10% (rs2293152 C/G, rs6503695 C/T, and rs9891119 A/C), representing 24 polymorphic sites of the STAT3 (r(2) > 0.8). We observed a significant association between mtDNA/nDNA ratio and both rs6503695 and rs9891119, adjusted by age and homeostasis model assessment index. The proportion of the total variance of the mtDNA/nDNA ratio accounted for by the rs6503695 and rs9891119 genotypes was 4.7% and 6.53%, respectively. Common variation in the STAT3 may influence mtDNA copy number.

Odor perception between heterosexual partners: its association with depression, anxiety, and genetic variation in odorant receptor OR7D4.

We performed a study on a sample of 856 individuals to answer whether the pleasantness/unpleasantness of the odor perception of their partners (rating of partner odor) is associated with depression and anxiety. To evaluate the influence of common genetic variation of the odorant receptor OR7D4 on the rating of partner odor, the variant rs8109935 was genotyped in the whole sample. The rating of partner odor was significantly associated with scores of anxiety and depression. Depression (OR: 0.75, 95% CI: 0.56-0.98, p = 0.039) and anxiety (Robust Coef ± SE: -13 ± 0.6, p = 0.044) were inversely associated with pleasantness rating of partner odor. Ordered probit regression analysis shows that the rating of partner odor was significantly associated with the rs8109935 genotypes (Coef ± robust SE: 0.19 ± 0.09, p = 0.028). These findings suggest that odor perception between heterosexual partners may have an impact on the development of depression and anxiety, and that it might be influenced by genetic variation in OR7D4.

High fat diet-induced liver steatosis promotes an increase in liver mitochondrial biogenesis in response to hypoxia.

Mitochondrial DNA (mtDNA) copy number plays a key role in the pathophysiology of metabolic syndrome-related phenotypes, but its role in non-alcoholic fatty liver disease (NAFLD) is not well understood. We evaluated the molecular mechanisms that may be involved in the regulation of liver mtDNA content in a high-fat-induced rat model of NAFLD. In particular, we tested the hypothesis that liver mtDNA copy number is associated with liver expression of HIF-1α. Rats were given either standard chow diet (SCD, n = 10) or high-fat diet (HFD, n = 15) for 20 weeks. Subsequently, mtDNA quantification using nuclear DNA (nDNA) as a reference was carried out using real time quantitative PCR. HFD induced a significant increase in liver mtDNA/nDNA ratio, which significantly correlated with the liver triglyceride content (R: 0.29, P < 0.05). The liver mtDNA/nDNA ratio significantly correlated with the hepatic expression of HIF-1α mRNA (R: 0.37, P < 0.001); liver HIF-1α mRNA was significantly higher in the HFD group. In addition, liver cytochrome c oxidase subunit IV isoform 1 (COX4I1) mRNA expression was also positively correlated with liver mtDNA content. The hepatic expression of mRNA of transcriptional factors that regulate mitochondrial biogenesis, including peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α) and PGC-1ß, nuclear respiratory factor-1 (NRF-1), peroxisome proliferator-activated receptor δ and Tfam, was not associated with the liver mtDNA content. Neither hepatocyte apoptosis nor oxidative stress was involved in the HIF-1α-mediated increase in mtDNA copy number. In conclusion, we found that HFD promotes an increase in liver mitochondrial biogenesis in response to hypoxia via HIF-1α, probably to enhance the mitochondrial function as well as to accommodate the metabolic load.

Gene-gene interaction between serotonin transporter (SLC6A4) and CLOCK modulates the risk of metabolic syndrome in rotating shiftworkers.

Serotonergic neurotransmission and the master circadian CLOCK gene are physiological modulators of the circadian system. In addition, both are involved in the physiopathology of metabolic syndrome (MS). The authors sought to examine the potential effect of the gene-gene interaction between the functional 44-bp insertion/deletion polymorphism in the promoter region (serotonin-transporter-linked promoter region polymorphism or 5-HTTLPR) of the serotonin transporter gene (SLC6A4) and common variants of the gene CLOCK on the genetic risk underlying MS of shift-workers. To test this hypothesis, 856 men were studied; 518 dayworkers were compared with 338 rotating shiftworkers. Medical history, health examination including anthropometric and arterial blood pressure measurements, a questionnaire on health-related behaviors, and biochemical determinations were obtained from every participant. 5-HTTLPR genotypes were determined using polymerase chain reaction followed by gel electrophoresis. Six tag single-nucleotide polymorphisms (SNPs) in the CLOCK gene with a minor allele frequency >10 % (rs1554483 C/G, rs11932595 A/G, rs4580704 C/G, rs6843722 A/C, rs6850524 C/G, and rs4864548 A/G), encompassing 117 kb of chromosome 4 and representing 115 polymorphic sites (r(2) > .8), were genotyped. A significant interaction between the 5-HTTLPR variant and the haplotype rs1554483-rs4864548 of the CLOCK gene was detected for diastolic (p = .0058) and systolic blood pressure (p = .0014), arterial hypertension (p = .033), plasma triglycerides levels (p = .033), and number of MS components (p = .01). In all these cases, the higher values were observed in rotating shiftworkers homozygous for the SLC6A4 S allele and carrying the haplotype composed by the CLOCK rs1554483 G and rs4864548 A variants. In conclusion, these data suggest a potential interaction (epistatic effect) of serotonin transporter and CLOCK gene variation on the genetic susceptibility to develop MS by rotating shiftworkers.

Methylation of TFAM gene promoter in peripheral white blood cells is associated with insulin resistance in adolescents.

PURPOSE: To explore whether DNA methylation of the mitochondrial transcription factor A (TFAM) promoter is associated with insulin resistance in a sample of adolescents with features of metabolic syndrome. METHODS: The data and blood samples were collected from 122 adolescents out of a cross-sectional study of 934 high-school students. The population was divided into two groups: noninsulin resistance (NIR) and insulin resistance (IR). After bisulfite treatment of genomic DNA from peripheral leukocytes, we used methylation-specific polymerase chain reaction (PCR) to assess DNA methylation of three putative methylation target sites (CpG) in the TFAM promoter. RESULTS: The ratio of the promoter methylated DNA/unmethylated DNA was 0.012+/-0.0009 (1.2% of alleles), and inversely correlated with the biochemical features of insulin resistance (plasma fasting insulin R: -0.26, p<0.004 and homeostasis model assessment (HOMA) index R: -0.27, p<0.002), and obesity (R: -0.27, p<0.002). Multiple regression analysis showed that the log-transformed HOMA index correlated with the status of promoter methylation of TFAM, independently of body mass index (BMI) Z score (beta: -0.33+/-0.094, p=0.00094). Finally, the TFAM promoter methylated DNA/unmethylated DNA ratio was found to be significantly associated with insulin resistance as dichotomous variable (NIR n=45, 0.014+/-0.002 and IR n=77, 0.011+/-0.001, respectively, p<0.016). CONCLUSION: Our findings suggest a potential role of promoter TFAM methylation in the pathogenesis of insulin resistance in adolescents.

Role of genetic variation in insulin-like growth factor 1 receptor on insulin resistance and arterial hypertension.

OBJECTIVE: To perform a two-stage study to explore the role of gene variants in the risk of insulin resistance and arterial hypertension. METHODS AND RESULTS: The selection of variants was performed by a first stage of in-silico analysis of the original genome-wide association data sets on genes involved in metabolic syndrome components, granted by the Diabetes Genetics Initiative and the Wellcome Trust Case-Control Consortium. We started by identifying single-nucleotide polymorphisms with a cutoff for association (P < 0.05) in both data sets after the application of a computational algorithm of gene prioritization. Among the more promising variants, six single-nucleotide polymorphisms in IGF1R (rs11247362, rs10902606, rs1317459, rs11854132, rs2684761, and rs2715416) were selected for further evaluation in our population. Altogether, 1094 men, aged 34.4 +/- 8.6 years, were included in a population-based study. Genotypes of rs2684761 showed significant association with insulin resistance (as a discrete trait, odds ratio per G allele 1.27, 95% confidence interval 1.03-1.56, P = 0.026; and homeostasis model assessment-insulin resistance as a continuous trait, P = 0.01). A significant association of rs2684761 with arterial hypertension was also observed (odds ratio per G allele 1.29, 95% confidence interval 1.02-1.64, P = 0.037) after adjusting for age and homeostasis model assessment-insulin resistance. CONCLUSION: Our study suggests for the first time a putative role of IGF1R variants in individual susceptibility to metabolic syndrome-related phenotypes, in particular on the risk of having insulin resistance and arterial hypertension.

Increased levels of resistin in rotating shift workers: a potential mediator of cardiovascular risk associated with circadian misalignment.

OBJECTIVE: Shift work schedule has been associated with several health problems, including deleterious effects on the cardiovascular system. The present study aimed to evaluate the circulating levels of four biomarkers of atherosclerosis (soluble CD40 ligand [sCD40L], monocyte chemoattractant protein-1 [MCP-1], resistin, and plasminogen activator inhibitor-1 [PAI-1]) in a population-based sample of young adult men exposed to rotating shift work schedule in comparison with day workers. DESIGN AND PARTICIPANTS: A total of 439 men aged 34.4+/-8.6 years were included in a cross-sectional study comparing 255 day workers with 184 rotating shift workers. Circulating levels of the biomarkers were measured in duplicate by ELISA using monoclonal specific antibodies. RESULTS: Rotating shift workers had elevated (6440+/-4510 pg/mL) (mean+/-SD) circulating levels of resistin in comparison with day workers (5450+/-3780 pg/mL), and significance remains after adjusting for age and blood leukocyte count (p<0.045, ANCOVA). Shift work schedule explains 1% of the proportion of the total variation in the circulating resistin levels. Multiple regression analysis showed that resistin levels significantly correlate with rotating shift work (p<0.04) and blood leukocyte count (p<0.00003) independently of age, BMI, waist-hip ratio, HOMA, and cardiovascular risk %. Circulating levels of sCD40L, MCP-1, and PAI-1 did not significantly differ between day workers and shift workers. CONCLUSION: Shift work schedule was significantly associated with elevated plasma resistin levels. Resistin, which is probably produced by leukocytes, may play an important role in the pathogenesis of early metabolic syndrome components in young men chronically exposed to circadian misalignment.

Circulating levels and hepatic expression of molecular mediators of atherosclerosis in nonalcoholic fatty liver disease.

OBJECTIVES: We evaluated circulating levels of biomarkers of atherosclerosis (soluble intercellular adhesion molecule: sICAM-1, plasminogen activator inhibitor: PAI-1 and soluble CD40 ligand: sCD40L) in patients with NAFLD proven through biopsy and control subjects, and correlated them with the histological disease severity. We further explored liver protein expression of ICAM-1, CD40 and PAI-1 in patients with different histological forms of NAFLD and control liver biopsies. PATIENTS AND METHODS: We included 215 individuals: 113 patients with NAFLD (simple steatosis n=45 and NASH n=68) and 102 control subjects. Circulating levels of the biomarkers were measured by ELISA. Liver expression of ICAM-1, CD40 and PAI-1 was assessed by immunohistochemistry using monoclonal antihuman antibodies. RESULTS: Patients with NAFLD, in comparison with control subjects, showed significantly higher circulating levels of sICAM-1 (605.3+/-34.6ng/ml vs. 356.5+/-24.6ng/ml, p=5.9 x 10(-6)), PAI-1 (22.8+/-1.7ng/ml vs. 19.0+/-2.1ng/ml, p=0.0149) and sCD40L (1347.5+/-513.7pg/ml vs. 804.5+/-396.1pg/ml, p=0.0229), results expressed as mean+/-SE. sICAM-1 was a strong predictor of histological severity of NAFLD, after adjusting for potential confounders. In addition, patients with NAFLD showed significantly higher liver staining scores for ICAM-1 and PAI-1 than control liver biopsies. ICAM-1 immunoreactivity in lobular inflammatory infiltrate showed high scores in NASH patients; a significant correlation was found between both the degree of liver steatosis and the severity of necroinflammatory activity and liver ICAM-1 expression. CONCLUSIONS: Our study shows that NAFLD is associated with elevated circulating levels and abnormal liver expression of molecular mediators of atherosclerosis. Additionally, ICAM-1 may be involved in liver damage and inflammation.

The nuclear receptor PXR gene variants are associated with liver injury in nonalcoholic fatty liver disease.

OBJECTIVE: To explore the contribution of gene variants and derived haplotypes of the pregnane X receptor (NR1I2) to the severity of nonalcoholic fatty liver disease (NAFLD). METHODS: A total of 290 individuals were evaluated in a case-control association study, including 188 NAFLD patients with different stages of disease severity and 102 healthy individuals. Four tag single nucleotide polymorphisms (SNPs; rs12488820 C/T, rs2472671 C/T, rs2461823 A/G, and rs1054191 A/G) encompassing 36 kb in chromosome 3 and representing 33 polymorphic sites (r2>0.8) were genotyped. Four additional SNPs (rs3814055, rs3814057, rs6785049, and rs7643645) were also included because they showed earlier evidence of functionality. RESULTS: Genotypic tests for single SNPs showed that rs7643645 and rs2461823 were significantly associated with disease severity by ordinal multinomial analysis (P<0.0015 and 0.039, respectively). A significant association was also observed under the additive model for both variants (P<0.00038 and 0.012, respectively). Consistent with the analysis of individual markers, we observed that the multimarker composed of rs2461823/A-rs7643645/G was significantly associated with disease severity (P<6.9 x 10(-5), beta: 0.45). In addition, the rs7643645/G variant was significantly associated with ALT level (P<0.026), a surrogate marker of severe liver injury. Finally, in univariate analysis rs7643645/G was significantly associated with fatty liver disease (P<0.04), with an odds ratio of 1.457 (95% confidence interval: 1.018-2.086). CONCLUSION: Our study suggests that pregnane X receptor polymorphisms and related haplotypes may contribute to disease severity in NAFLD by influencing the individual susceptibility to progress to more severe stages of the disease.

A nonsynonymous gene variant in the adiponutrin gene is associated with nonalcoholic fatty liver disease severity.

We explored the role of the adiponutrin (PNPLA3) nonsynonymous-rs738409 single nucleotide polymorphism (SNP) in genetic susceptibility to nonalcoholic fatty liver disease (NAFLD) and whether this SNP contributes to the severity of histological disease. Two hundred sixty-six individuals were evaluated in a case-control association study, which included 172 patients with features of NAFLD and 94 control subjects. The rs738409 G allele was significantly associated with NAFLD (P < 0.001; OR 2.8 95%, CI 1.5-5.2), independent of age, sex, body mass index (BMI), and Homeostasis Model Assessment (HOMA) index. When we tested the hypothesis of a relation between the SNP and the histological spectrum of NAFLD, a significant association was observed [chi2 19.9, degree of freedom (df): 2, P < 5 x 10(-5), adjusted for HOMA and BMI]. The degree of liver steatosis, as evaluated by liver biopsy, was significantly associated with the rs738409 G allele. Patients with CC genotype showed a lower steatosis score (14.9% +/- 3.9) in comparison with the CG genotype (26.3% +/- 3.5) and GG genotype (33.3% +/- 4.0) (P < 0.005). The proportion of the total variation attributed to rs738409 genotypes was 5.3% (beta 0.23 +/- 0.07; P < 0.002). Our data suggest that the rs738409 G allele is associated not only with fat accumulation in the liver but also with liver injury, possibly triggered by lipotoxicity.

Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes.

PURPOSE: We present an approach to prioritize single nucleotide polymorphisms for further follow-up in genome-wide association studies of type 2 diabetes. METHOD: The proposed method combines both the use of open data access from two type 2 diabetes-genome-wide association studies (granted by the Diabetes Genetics Initiative and the Welcome Trust Case Control Consortium) and the comprehensive analysis of candidate regions generated by the freely accessible ENDEAVOUR software. RESULTS: The algorithm prioritized all genes of the whole genome in relation to type 2 diabetes. There were six of 1096 single nucleotide polymorphisms in five genes potentially associated with type 2 diabetes: tachykinin receptor 3 (rs1384401), anaplastic lymphoma receptor tyrosine kinase (rs4319896), calcium channel, voltage-dependent, L type, alpha 1D subunit (rs12487452), FOXO1A (rs10507486 and rs7323267), and v-akt murine thymoma viral oncogene homolog 3 (rs897959). We estimated the fixed effect and P values of each single nucleotide polymorphism in the combined dataset by Mantel-Haenszel meta-analysis and we observed significant P values for all single nucleotide polymorphisms except for rs897959 at v-akt murine thymoma viral oncogene homolog 3. CONCLUSION: The proposed strategy may be used as an alternative tool for optimizing the information of the nearly 500,000 gene variants in which markers with modest significant P value for disease association are currently disregarded. Additionally, the said single nucleotide polymorphisms may be incorporated into the replication of the multistage design involved in the genome-wide association studies.

A diagnostic model to differentiate simple steatosis from nonalcoholic steatohepatitis based on the likelihood ratio form of Bayes theorem.

OBJECTIVE: To evaluate the performance of a diagnostic model based on a composite index using clinical and laboratory data, including cardiovascular biomarkers, to help practitioners to differentiate patients with simple steatosis from those with nonalcoholic steatohepatitis (NASH). DESIGN AND METHODS: 101 patients with biopsy proven features of nonalcoholic fatty liver disease were included. We investigated the usefulness of 9 biomarkers in predicting the histological disease severity, including routine biochemical tests, C-reactive protein, soluble intercellular adhesion molecule-1 (sICAM-1) and anthropometric evaluation. Receiver operating characteristic (ROC) curves and likelihood ratios (LRs) were used to evaluate the fit of each test. A composite index was calculated as the product of each individual test LR. RESULTS: In a model patient who has all positive tests, the post-test probability for NASH would be 99.5%. CONCLUSION: The capacity of each individual biomarker to independently predict the disease outcome was lower than a composite index constructed after multiplying the LR for each individual test combined into a "multimarker" score.

Polymorphisms of MRP2 (ABCC2) are associated with susceptibility to nonalcoholic fatty liver disease.

AIMS: We hypothesized that ABCC2 gene variants may contribute to susceptibility to nonalcoholic fatty liver disease (NAFLD). Additionally, we tested the hypothesis of a relation between gene variants and disease severity. PATIENTS AND METHODS: The study involved 167 individuals: 109 consecutively presenting unrelated patients with features of NAFLD and different stages of disease severity, and a group of 58 healthy individuals. Four tag single-nucleotide polymorphisms (SNPs; rs717620 A/G, rs2756105 C/T, rs2002042 C/T and rs3740066 A/G) representing 46 polymorphic sites (r(2)>.8) were genotyped. Furthermore, two additional SNPs (rs17222723 A/T and rs8187710 G/A) were included. RESULTS: On univariate analysis, after multiple comparison correction by permutation tests, there were significant differences observed in the allele frequencies of rs17222723 and rs8187710 between healthy individuals and NAFLD patients (empirical P=.037 and .035, respectively). Allelic odds ratios [95% confidence interval] for rs17222723 and rs8187710 were 2.80 [1.11-7.04] and 2.80 [1.11-7.04], respectively. When we tested the hypothesis of a relation between gene variants and the clinical and histological spectra of NAFLD by multinomial regression analysis, a significant association was observed with the same markers: rs17222723 (P=.0029) and rs8187710 (P=.015). CONCLUSIONS: Our study suggests a potential role of ABCC2 in susceptibility to NAFLD and disease severity.

Genetic variants in STAT3 are associated with nonalcoholic fatty liver disease.

AIMS: To investigate the role of gene variants and derived haplotypes of the STAT3 transcription factor in nonalcoholic fatty liver disease (NAFLD) and their relation with the clinical disease severity. PATIENTS AND METHODS: 108 patients with NAFLD and different stages of clinical disease severity, and a group of 55 healthy individuals were included in a Hospital-based study. We selected 3 tagSNPs showing a minor allele frequency >10% (rs2293152 C/G, rs6503695 C/T, and rs9891119 A/C) encompassing 68.55kb in chromosome 17, representing 24 polymorphic sites (r(2)>0.8). RESULTS: In univariate analysis, there were significant differences in the allele frequency of the rs6503695 and rs9891119 between the healthy individuals and NAFLD patients (empiric P=0.021 and 0.020, respectively). The test results for the multi-marker analysis showed that haplotypes TA and CC of tagSNPs rs6503695, rs9891119 were significantly associated with NAFLD (empiric P=0.035 and 0.015, respectively). When we tested the hypothesis of a relation between the gene variants and the clinical and histological spectrum of NAFLD by multinomial analysis, a significant association was observed with rs9891119 (P=0.02). CONCLUSIONS: Our study suggests a potential role of the STAT3 polymorphisms and their haplotypes in susceptibility to NAFLD and disease severity.

Genetic variants of Clock transcription factor are associated with individual susceptibility to obesity.

BACKGROUND: Altering circadian rhythmicity results in pathophysiologic changes resembling metabolic syndrome and fat accumulation. OBJECTIVE: We investigated the role of gene variants and derived haplotypes of the CLOCK transcription factor in obesity and related quantitative metabolic traits. DESIGN: Lean (n = 715) and overweight or obese (n = 391) unrelated subjects aged 34.4 +/- 8.6 y were included in a population-based cross-sectional study. Six tag single-nucleotide polymorphisms (SNPs) with a minor (>10%) allele frequency (rs1554483 C/G; rs11932595 A/G; rs4580704 C/G; rs6843722 A/C; rs6850524 C/G, and rs4864548 A/G) encompassing 117 kb of chromosome 4 and representing 115 polymorphic sites (r(2) > 0.8) were genotyped. Association was tested by PLINK and WHAP software, and multiple testing was controlled by permutation test. RESULTS: The genotype frequencies of 4 tag SNPs--rs1554483, rs6843722, rs6850524, and rs4864548--had significant (empiric P < 0.010, 0.021, 0.021, and 0.010, respectively) associations with overweight or obesity. Haplotype analysis showed that only paired haplotypes, including rs1554483 and rs4864548, had a significant effect on overweight or obesity. Combinations of these SNPs (haplotype block CG and GA) are responsible for the gene effect (GA frequencies: 47% in cases, 41% in controls; empiric P < 0.011). These findings were concurrently observed in a sample of persons from a hospital-based study, and the combined Mantel-Haenszel fixed effect was an odds ratio of 1.82 (95% CI: 1.31, 2.54; P < 0.001) for the paired haplotype, which included CG and GA for rs1554483 and rs4864548. CONCLUSIONS: The present study suggests a putative role of the CLOCK polymorphism and related haplotypes in susceptibility to obesity. The haplotype of rs1554483G and rs4864548A was associated with a 1.8-fold risk of overweight or obesity.